Comparing co-evolution methods and their application to template-free protein structure prediction.

ABSTRACT:

Motivation

Co-evolution methods have been used as contact predictors to identify pairs of residues that share spatial proximity. Such contact predictors have been compared in terms of the precision of their predictions, but there is no study that compares their usefulness to model generation.

Results

We compared eight different co-evolution methods for a set of ∼3500 proteins and found that metaPSICOV stage 2 produces, on average, the most precise predictions. Precision of all the methods is dependent on SCOP class, with most methods predicting contacts in all α and membrane proteins poorly. The contact predictions were then used to assist in de novo model generation. We found that it was not the method with the highest average precision, but rather metaPSICOV stage 1 predic

SUBMITTER: de Oliveira SH 

PROVIDER: S-EPMC5860252 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature